Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Live cell monitoring of periodic gene expression in synchronous human cells identifies forkhead genes involved in cell cycle control

ABSTRACT: We report the genome wide DNA binding patterns of wild type FOXK1 in asynchronous HeLa cells using chromatin precipitation followed by high-throughput sequencing (ChIP-seq). We find that FOXK1 is bound to the promoter of a number of cell cycle genes including the E2F binding partner TFDP1. This study is the first reported study of FOXK1 binding on a genome-wide scale in HeLa cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE39138 | GEO | 2012/07/09

SECONDARY ACCESSION(S): PRJNA170078

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Live cell monitoring of periodic gene expression in synchronous human cells identifies forkhead genes involved in cell cycle control

Project description:We report the genome wide DNA binding patterns of wild type FOXK1 in asynchronous HeLa cells using chromatin precipitation followed by high-throughput sequencing (ChIP-seq). We find that FOXK1 is bound to the promoter of a number of cell cycle genes including the E2F binding partner TFDP1. This study is the first reported study of FOXK1 binding on a genome-wide scale in HeLa cells. Chromatin precipitation

2012-07-09 | E-GEOD-39138 | biostudies-arrayexpress

Live-cell monitoring of periodic gene expression in synchronous human cells identifies Forkhead genes involved in cell cycle control.

Project description: Not available

| S-EPMC3418304 | biostudies-literature

Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors [ChIP-seq]

Project description:We report the genome wide DNA binding patterns of wild type FOXM1 in asynchronous HeLa cells using chromatin precipitation followed by high-throughput sequencing (ChIP-seq). We find that FOXM1 is bound to the promoter of a number of cell cycle genes including PLK, AURKB, and CCNB1. FOXM1 ChIP-seq in asynchronous HeLa cells

2013-11-06 | E-GEOD-52098 | biostudies-arrayexpress

Comparative transcriptomic analysis of WT, FOXK1/2 KO, DKO cells and FOXK1 KO cells with reconstitution of several FOXK1 mutants

Project description:The goal of this study was to apply Next Generation Sequencing analyses to identify genes and pathways regulated by the FOXK1 and FOXK2 transcription factor in HeLa cells and to see whether reconstitution of FOXK1 WT and mutants can rescue the altered gene regulation in FOXK1 KO cells. Gene Ontology (GO) analysis did not uncover any dysregulated DNA damage–related pathways upon FOXKs KO. We found that cells reconstituted with any of the three FOXK1 mutants could largely rescue dysregulated gene expression in FOXK1 KO cells, similar to cells reconstituted with WT FOXK1. These suggesting that FOXK1's role in DNA damage response is not by direct transcriptional regulation of DNA damage related pathways and all the three FOXK1 mutants could not affect transcription.

2020-06-26 | GSE151029 | GEO

Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors [ChIP-seq]

2013-11-06 | GSE52098 | GEO

A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

2015-04-10 | GSE52170 | GEO

A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis in Schizosaccharomyces pombe, Schizosaccharomyces octosporus, Schizosaccharomyces japonicus and Saccharomyces cerevisiae Samples from mononucleosomal DNA from asynchronous mitosis of four species of budding (Saccharomyces cerevisiae W303-1a) and fission yeasts (S. pombe wild type 972h-, S. octosporus CBS1804, S. japonicus var. japonicus ade12- FY53) were sequenced (Illumina Genome Analyzer IIx and HiSeq 2500) using the single read and paired end protocol.

2015-04-10 | E-GEOD-52170 | biostudies-arrayexpress

RNA-seq of human embryonic stem cells H1 ESC cells and the differentiated NPC cells with FOXK1/2 and SIN3A knock down and the control condition.

Project description:In order to investigate the genome-wide binding profile of the forkhead transcription factor FOXK2 in human embryonic stem cells (ESCs) and downstream cell types, we generated the RNA-seq data with FOXK1/2 and SIN3A siRNA in H1 ESC cells and FOXK1/2 siRNA in the differentiated NPC cells.

2021-09-08 | E-MTAB-9639 | biostudies-arrayexpress

Epigenetic and transcriptional regulation of starvation-induced atrophy and autophagy programs by Foxk1 and Sin3A

Project description:Autophagy is the primary catabolic process triggered in response to starvation. Although autophagic regulation within the cytosolic compartment is well established, it is becoming clear that nuclear events also regulate the induction or repression of autophagy. Nevertheless, a thorough understanding of the mechanisms by which sequence-specific transcription factors modulate expression of genes required for autophagy is lacking. Here, we identify Foxk proteins (Foxk1 and Foxk2) as transcriptional repressors of autophagy in muscle cells and fibroblasts. Interestingly, Foxk1/2 serve to counter-balance another forkhead transcription factor, Foxo3, which induces an overlapping set of autophagic and atrophic targets in muscle. Foxk1/2 specifically recruits Sin3A-HDAC complexes to restrict acetylation of histone H4 and expression of critical autophagy genes. Remarkably, mTOR promotes the transcriptional activity of Foxk1 by facilitating nuclear entry to specifically limit basal levels of autophagy in nutrient-rich conditions. Our study highlights an ancient, conserved mechanism whereby nutritional status is interpreted by mTOR to restrict autophagy by repressing essential autophagy genes via Foxk-Sin3-mediated transcriptional control. Examination of (1) chromatin binding of Foxk1 and Sin3A in non-starved myoblasts and (2) gene expression profiling upon either starvation or siRNA-mediated depletion of Foxk1 relative to a non-starved control.

2014-11-17 | E-GEOD-56932 | biostudies-arrayexpress

Extensive profiling of Foxk1 binding in genomic DNA

Project description:We report DNA binding of a transcription factor Foxk1 in globle genomic DNA

2018-04-05 | GSE112709 | GEO